Abstract <p>The study objects are represented by calcareous and weakly differentiated soils underlain by hard calcareous–silicate rocks (red-colored and without reddish pigment) formed in the cold continental environment of the southern part of the Lena-Angara Plateau, Eastern Siberia. The study aim is to investigate the autochthonous/allochthonous nature of the loose calcareous substrate underlain by the hard rock, using data of clay mineralogy. Intensive leaching of carbonates in the soil profiles caused a decrease in pH values simultaneously with an increase in the proportions of dithionite extractable iron in the topsoil. The clay mineral association is the same in the red-colored soil and calcareous hard rock. It is represented by chlorite and dioctahedral mica (illite) and by a small proportion of the mixed-layer illite–smectite (vermiculite) structures with &lt;50% of smectite (vermiculite) layers. The latter slightly increases in the soil horizons as compared to the hard rock. Oppositely, clay mineralogy in the profile on the non-reddish-colored rock differs from that in the silicate part of the hard rock. Dioctahedral smectite, talc, dioctahedral mica, chlorite, and mixed-layer chlorite–vermiculite (smectite) were identified in the silicate part of the calcareous hard rock. The proportions of talc and smectitic clay in the soil horizons decreased. In addition, the appearance of kaolinite in the soil horizons, which is absent in the hard rock, may be an indicator of the allochthonous substrate admixture. The studied soils reflect two variants of pedogenesis on the loose calcareous substrate underlain by hard calcareous–silicate rocks: (i) on the eluvium of hard rock (red-colored profile) and (ii) with admixture of allochthonous loose substrate in the profile underlain by hard calcareous rock.</p>